[gmx-users] Mean Square Displacement: gromacs 4.5 Vs gromacs 4.6.1

rajat desikan rajatdesikan at gmail.com
Fri Aug 2 22:43:13 CEST 2013

Hi, are you referring to the MSD of the protein?
I am not sure which of the MSDs are right, or why there is a difference
between the two versions. But, both of the MSDs are plausible. There is no
obvious wrong answer. Complex molecules have a long time relaxation and may
exhibit glassy behavior and thus an MSD like the blue line. Look at this
reference which shows that lipids exhibit sub-diffusive behavior till 30
ns. Protein dynamics are never straightforward.
There is a valid issue about the discrepancy between the two versions.
Others may be able to help you here. I suggest longer simulations.

On Fri, Aug 2, 2013 at 9:20 PM, Guillaume Chevrot
<gchevrot at cnrs-orleans.fr>wrote:

> Hi,
> I performed 2 simulations of a lysozyme in water: one with the version 4.5
> of Gromacs and another with the version 4.6.1 (I used the exact same
> inputs).
> Then I calculated the MSD and I obtained a complete different behavior with
> the version 4.6.1 of Gromacs and this MSD is obviously wrong.
> <http://gromacs.5086.x6.nabble.com/file/n5010317/MSD_gmxList.jpg>
> Do you have any ideas what I am doing wrong or did you encounter such a
> behavior?
> Regards,
> Guillaume
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore

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